Examples with IKnowledge edu.cmu.tetrad.data.IKnowledge used on opensource projects

Example 41 with IKnowledge

use of edu.cmu.tetrad.data.IKnowledge in project tetrad by cmu-phil.

the class FciRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    Graph graph;
    if (getParams().getBoolean("rfciUsed", false)) {
        Rfci fci = new Rfci(getIndependenceTest());
        fci.setKnowledge(knowledge);
        fci.setCompleteRuleSetUsed(getParams().getBoolean("completeRuleSetUsed", false));
        fci.setMaxPathLength(getParams().getInt("maxReachablePathLength", -1));
        fci.setDepth(getParams().getInt("depth", -1));
        graph = fci.search();
    } else {
        Fci fci = new Fci(getIndependenceTest());
        fci.setKnowledge(knowledge);
        fci.setCompleteRuleSetUsed(getParams().getBoolean("completeRuleSetUsed", false));
        fci.setPossibleDsepSearchDone(getParams().getBoolean("possibleDsepDone", true));
        fci.setMaxPathLength(getParams().getInt("maxReachablePathLength", -1));
        fci.setDepth(getParams().getInt("depth", -1));
        graph = fci.search();
    }
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}

Example 42 with IKnowledge

use of edu.cmu.tetrad.data.IKnowledge in project tetrad by cmu-phil.

the class PcStableRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    int depth = getParams().getInt("depth", -1);
    PcStable pc = new PcStable(getIndependenceTest());
    pc.setKnowledge(knowledge);
    pc.setAggressivelyPreventCycles(isAggressivelyPreventCycles());
    pc.setDepth(depth);
    pc.setInitialGraph(initialGraph);
    Graph graph = pc.search();
    System.out.println(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}

Example 43 with IKnowledge

use of edu.cmu.tetrad.data.IKnowledge in project tetrad by cmu-phil.

the class YeastPcCcdSearchWrapper method main.

public static void main(String[] args) {
    int[][] yeastReg = { { 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0 }, { 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0 }, { 1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1 }, { 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1 }, { 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0 }, { 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0 }, { 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1 }, { 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0 }, { 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1 }, { 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0 }, { 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1 } };
    List listOfNames = new ArrayList();
    // get the file containing the file names
    DataSet cds = null;
    try {
        DataReader reader = new DataReader();
        cds = reader.parseTabular(new File(args[0]));
    } catch (IOException e) {
        e.printStackTrace();
    }
    String outfileprefix = args[1];
    String outverbosefile = outfileprefix + ".doc";
    String outsummaryfile = outfileprefix + ".xls";
    OutputStream s1 = null;
    OutputStream s2 = null;
    boolean verbose = true;
    try {
        s1 = new FileOutputStream(outverbosefile);
    } catch (IOException e) {
        System.out.println("Cannot open file file " + outverbosefile);
        System.exit(0);
    }
    DataOutputStream d1 = new DataOutputStream(s1);
    try {
        s2 = new FileOutputStream(outsummaryfile);
    } catch (IOException e) {
        System.out.println("Cannot open file file " + outsummaryfile);
        System.exit(0);
    }
    DataOutputStream d2 = new DataOutputStream(s2);
    try {
        // if(!verbose) {
        d2.writeBytes("File\tPC05 FP\tPC05 FN\tPC10 FP\tPC10 FN\tPC15 FP\t");
        d2.writeBytes("PC15 FN\tPC20 FP\tPC20 FN\tPC30 FP\tPC30 FN\t");
        d2.writeBytes("CCD05 FP\tCCD05 FN\tCCD10 FP\tCCD10 FN\tCCD 15 FP\t");
        d2.writeBytes("CCD15 FN\tCCD20 FP\tCCD20 FN\tCCD30 FP\tCCD 30 FN\n");
        // }
        // read in variable name and set up DataSet.
        // RectangularDataSet dataSet = DataLoaders.loadContinuousData(
        // new File(args[0]), DelimiterType.WHITESPACE,
        // "//"
        // );
        // int ngenes = 6;
        int ngenes = Integer.valueOf(args[2]);
        IKnowledge bk = new Knowledge2();
        bk.addToTiersByVarNames(listOfNames);
        // if(verbose) {
        d1.writeBytes("\n \n**Results for data in file yeastTRN**\n \n");
        d1.writeBytes("  Acutal adj matrix: \n");
        printAdjMatrix(yeastReg, listOfNames, d1);
        // }
        int[] PC05Accuracy;
        PC05Accuracy = PCAccuracy(0.05, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] PC10Accuracy;
        PC10Accuracy = PCAccuracy(0.10, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] PC15Accuracy;
        PC15Accuracy = PCAccuracy(0.15, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] PC20Accuracy;
        PC20Accuracy = PCAccuracy(0.20, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] PC30Accuracy;
        PC30Accuracy = PCAccuracy(0.30, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] CCD05Accuracy;
        CCD05Accuracy = CcdAccuracy(0.05, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] CCD10Accuracy;
        CCD10Accuracy = CcdAccuracy(0.10, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] CCD15Accuracy;
        CCD15Accuracy = CcdAccuracy(0.15, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] CCD20Accuracy;
        CCD20Accuracy = CcdAccuracy(0.20, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        int[] CCD30Accuracy;
        CCD30Accuracy = CcdAccuracy(0.30, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);
        /*
            int[] FCI05Accuracy;
            FCI05Accuracy =
              FCIAccuracy(0.05, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);

            int[] FCI10Accuracy;
            FCI10Accuracy =
              FCIAccuracy(0.10, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);

            int[] FCI15Accuracy;
            FCI15Accuracy =
              FCIAccuracy(0.15, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);

            int[] FCI20Accuracy;
            FCI20Accuracy =
              FCIAccuracy(0.20, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);

            int[] FCI30Accuracy;
            FCI30Accuracy =
              FCIAccuracy(0.30, ngenes, cds, bk, yeastReg, listOfNames, d1, verbose);


            */
        // if(!verbose) {
        d2.writeBytes("yeastTRN \t");
        d2.writeBytes(PC05Accuracy[0] + "\t");
        d2.writeBytes(PC05Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(PC10Accuracy[0] + "\t");
        d2.writeBytes(PC10Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(PC15Accuracy[0] + "\t");
        d2.writeBytes(PC15Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(PC20Accuracy[0] + "\t");
        d2.writeBytes(PC20Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(PC30Accuracy[0] + "\t");
        d2.writeBytes(PC30Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(CCD05Accuracy[0] + "\t");
        d2.writeBytes(CCD05Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(CCD10Accuracy[0] + "\t");
        d2.writeBytes(CCD10Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(CCD15Accuracy[0] + "\t");
        d2.writeBytes(CCD15Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(CCD20Accuracy[0] + "\t");
        d2.writeBytes(CCD20Accuracy[1] + "\t");
        // }
        // if(!verbose) {
        d2.writeBytes(CCD30Accuracy[0] + "\t");
        d2.writeBytes(CCD30Accuracy[1] + "\n");
    // }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 44 with IKnowledge

use of edu.cmu.tetrad.data.IKnowledge in project tetrad by cmu-phil.

the class KnowledgeBoxEditor method resetEdgeDisplayOld.

/**
 * This is an old method that needs to be removed when cleaning up code.
 */
private void resetEdgeDisplayOld() {
    List<String> varNames = getVarNames();
    IKnowledge knowledge = getKnowledge();
    for (String name : varNames) {
        knowledge.addVariable(name);
    }
    KnowledgeGraph graph = new KnowledgeGraph(getKnowledge());
    for (String varName : varNames) {
        graph.addNode(new KnowledgeModelNode(varName));
    }
    if (this.showRequiredByGroups) {
        for (Iterator<KnowledgeEdge> i = knowledge.requiredEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge edge = i.next();
            String from = edge.getFrom();
            String to = edge.getTo();
            if (knowledge.isRequiredByGroups(from, to)) {
                KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
                KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
                graph.addEdge(new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.REQUIRED_BY_GROUPS));
            }
        }
    }
    if (this.showForbiddenByGroups) {
        for (Iterator<KnowledgeEdge> i = knowledge.forbiddenEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge edge = i.next();
            String from = edge.getFrom();
            String to = edge.getTo();
            if (knowledge.isForbiddenByGroups(from, to)) {
                KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
                KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
                graph.addEdge(new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.FORBIDDEN_BY_GROUPS));
            }
        }
    }
    if (showRequired) {
        for (Iterator<KnowledgeEdge> i = knowledge.explicitlyRequiredEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge pair = i.next();
            String from = pair.getFrom();
            String to = pair.getTo();
            KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
            KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
            if (fromNode == null || toNode == null) {
                continue;
            }
            graph.addEdge(new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.REQUIRED));
        }
    }
    if (showForbiddenByTiers) {
        for (Iterator<KnowledgeEdge> i = knowledge.forbiddenEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge pair = i.next();
            String from = pair.getFrom();
            String to = pair.getTo();
            if (!knowledge.isForbiddenByTiers(from, to)) {
                continue;
            }
            KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
            KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
            if (fromNode == null) {
                graph.addNode(new KnowledgeModelNode(from));
                fromNode = (KnowledgeModelNode) graph.getNode(from);
            }
            if (toNode == null) {
                graph.addNode(new KnowledgeModelNode(to));
                toNode = (KnowledgeModelNode) graph.getNode(to);
            }
            KnowledgeModelEdge knowledgeModelEdge = new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.FORBIDDEN_BY_TIERS);
            graph.addEdge(knowledgeModelEdge);
        // Hacked fix. Jdramsey.
        // if (!graph.containsEdge(knowledgeModelEdge)) {
        // graph.addEdge(knowledgeModelEdge);
        // }
        }
    }
    if (showForbiddenExplicitly) {
        for (Iterator<KnowledgeEdge> i = knowledge.explicitlyForbiddenEdgesIterator(); i.hasNext(); ) {
            KnowledgeEdge pair = i.next();
            String from = pair.getFrom();
            String to = pair.getTo();
            KnowledgeModelNode fromNode = (KnowledgeModelNode) graph.getNode(from);
            KnowledgeModelNode toNode = (KnowledgeModelNode) graph.getNode(to);
            KnowledgeModelEdge edge = new KnowledgeModelEdge(fromNode, toNode, KnowledgeModelEdge.FORBIDDEN_EXPLICITLY);
            if (!graph.containsEdge(edge)) {
                graph.addEdge(edge);
            }
        }
    }
    boolean arrangedAll = GraphUtils.arrangeBySourceGraph(graph, edgeWorkbench.getGraph());
    if (!arrangedAll) {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    edgeWorkbench.setGraph(graph);
    if (knowledgeBoxModel != null) {
        notifyKnowledge();
    }
}

Example 45 with IKnowledge

use of edu.cmu.tetrad.data.IKnowledge in project tetrad by cmu-phil.

the class CfciRunner method execute.

// =================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    Parameters searchParams = getParams();
    Parameters params = searchParams;
    Cfci cfci = new Cfci(getIndependenceTest());
    cfci.setKnowledge(knowledge);
    cfci.setDepth(params.getInt("depth", -1));
    Graph graph = cfci.search();
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}